Biology subjects

Kang, R.

Publications and source records attributed to Kang, R..

15 recordsLinked to original sources

bioRxiv2026

Female-Biased IL-17/STAT3 Signaling Marks Dementia-Associated Microglial Inflammation in Alzheimer's Disease

INTRODUCTION: Alzheimer's disease (AD) disproportionately affects women, but the underlying mechanisms are not fully understood. We compare sex-specific molecular changes across AD with and without dementia at single-cell resolution. METHODS: We performed sex-stratified single-nucleus transcriptomic analysis of human AD to dissect sex-specific differences in dementia progression, using the SEA-AD cohort for discovery and the ROSMAP and NBB datasets, together with 5xFAD mouse models, for validation. Donors were classified as no-dementia controls, no-dementia AD, or dementia AD, followed by donor-level pathway analysis, de novo microglial clustering, communication modeling, and cytokine-response enrichment RESULTS: Females with AD dementia showed enhanced inflammatory pathway activity across glial, neuronal and vascular-associated cell types, with the strongest enrichment in microglia. This female-biased program centered on IL6-JAK-STAT3 signaling and increased STAT3 expression in microglia and astrocytes. These results were validated in the ROSMAP and NBB datasets and conserved in the 5xFAD mouse model. Microglial clustering resolved 18 states and revealed sex-divergent disease remodeling, including female-specific expansion of redox-reactive and CD163+ macrophage-primed states. Cell:cell communication analysis identified female-biased TGF{beta}/GRN signaling, male-biased CD99 signaling, and dementia-associated SPP1-integrin communication with the vasculature. Microglial cytokine-response analysis identified IL-2 response as a dementia-associated signature in both sexes, alongside a female-biased IL-17/interferon response and a male-biased IL-7 response. DISCUSSION: These findings identify a disease-emergent, female-biased STAT3-centered neuroinflammatory program in human and mouse AD, linking sex-specific microglial remodeling to cytokine responsiveness and glial-vascular communication. The results suggest that sex-specific changes in neuroinflammation pathways in microglia and other cell types are associated with progression to dementia.

neuroscience↗

bioRxiv2026

Harmine Plus Exendin-4 Enhances Remission of Recent-Onset Type 1 Diabetes Following Anti-CD3 Therapy

Type 1 diabetes (T1D) results from autoimmune destruction of pancreatic {beta}-cells. While anti-CD3 therapy can delay disease progression and preserve residual {beta}-cell function, disease reversal will likely require both immune modulation and {beta}-cell regeneration. We found that the combination of harmine and exendin-4 (H+E) reduced inflammation-induced human {beta}-cell apoptosis, suppressed cytokine signaling and immunogenicity pathways, and improved {beta}-cell function. Although H+E alone did not reverse diabetes in NOD mice, low-dose anti-CD3 followed by H+E normalized blood glucose, increased insulin levels, improved glucose tolerance, expanded {beta}-cell mass, and enhanced diabetes remission. These effects were associated with reduced pro-inflammatory T-cell responses, increased regulatory T cells, and greater expression of exhaustion-related T-cell markers, without broad lymphocyte depletion. Similar immunomodulatory effects were observed in activated human PBMCs. Transcriptomic analyses identified the lncRNA SNHG6 as a key mediator of H+E action; SNHG6 protected {beta}-cells from cytokine-induced stress, apoptosis, and immunogenicity. Together, these findings demonstrate that H+E promotes {beta}-cell recovery and resilience while reducing {beta}-cell immunogenicity, enabling remission of recent-onset T1D when combined with anti-CD3 therapy. SNHG6 emerges as a novel regulator of {beta}-cell protection during inflammation.

cell biology↗

bioRxiv2026

Cryptic disease-prone states in human mesocortical assembloids revealed by multimodal profiling

Neurodegenerative diseases are characterized by synaptic failure, aberrant protein accumulation, and neuroglial dysfunction that emerge long before clinical onset. Although brain assembloids, which recapitulate interregional circuit connectivity beyond the scope of single organoids, significantly advance the modeling of circuit pathophysiology, they are predominantly evaluated through single-modality approaches that cannot resolve the functional and molecular heterogeneity underlying differential disease susceptibility. Here we show that morphologically identical human iPSC-derived dorso forebrain-midbrain mesocortical assembloids (MCAs) spontaneously bifurcate into disease-prone and non-prone states under identical culture conditions, revealing that MCA heterogeneity reflects intrinsic neurodegeneration susceptibility rather than stochastic culture variability. Using integrated electrophysiological, molecular, and spatial profiling, we find that disease-prone MCAs exhibit a temporally ordered molecular cascade in which neurofilament light chain elevation precedes tau dysregulation, mirroring the sequential biomarker trajectories observed in pre-symptomatic human neurodegeneration. Disease-prone MCAs further display selective cortical hyperexcitability and aberrant brainwave-like oscillatory dynamics that remain undetectable by any single modality. Spatially, a discrete junction-like neuronal population at the midbrain-forebrain interface shows transcriptional priming for synaptic overactivation alongside impaired astrocytic glutamate clearance, defining a spatially confined neuron-glial uncoupling as a candidate early origin of the disease-prone state. These findings reframe MCA heterogeneity as a biological window into pre-symptomatic neurodegeneration, with broad implications for disease modeling, risk stratification, and therapeutic discovery.

neuroscience↗

bioRxiv2025

An increase of NPY1 expression leads to inhibitory phosphorylation of PIN-FORMED (PIN) proteins and suppression of pinoid (pid) null mutants

The PINOID (PID) protein kinase is required for flower initiation in Arabidopsis. The pid mutants fail to initiate flowers on inflorescences, a phenotype that is mimicked by disrupting either the NAKED PINS IN YUC MUTANTS (NPY) gene family or PIN FORMED 1 (PIN1). Both PID and NPY1 have been reported to positively modulate PIN-mediated polar auxin transport. Here, we show that overexpression of NPY1 (NPY1 OE) completely suppressed pid null mutants, demonstrating that NPY1 functions downstream of PID. NPY1 OE triggered phosphorylation of PIN proteins at multiple sites that are mostly different from the previously characterized phosphorylation sites regardless of the presence of PID. Phosphorylation of the newly identified PIN sites in NPY1 OE plants likely leads to the inhibition of PIN functions, as we previously showed that pid is suppressed by decreasing PIN1 gene dosage or decreasing PIN1 activity. Furthermore, we show that the Ser/Thr rich C-terminal motif in NPY1 is phosphorylated and is required for pid suppression by NPY1 OE. Overexpression of NPY1 that lacked the C-terminal motif (NPY1{Delta}C) failed to rescue pid, but overexpression of NPY1{Delta}C was still able to trigger phosphorylation of PIN proteins including PIN2, which is known to cause agravitropic roots when mutated. NPY1{Delta}C overexpression plants displayed a complete loss of root gravitropic response, likely caused by PIN2 phosphorylation. Our results suggest a pathway for auxin mediated-flower initiation, in which PID regulates NPY1 accumulation and/or activity, and subsequently, NPY1 triggers phosphorylation of PIN proteins and inhibition of PIN functions.

plant biology↗

bioRxiv2025

Nutrient excess remodels islet autonomic innervation via pancreatic schwann cells

Nutrient excess results in short- and long-term adaptations in the structure and function of metabolic organs, such as pancreatic islets. Pancreatic innervation contributes to islet architecture and function in many species, including humans, but little is known about its adaptation to over-nutrition. Here, we use 3D imaging to show that short-term high fat diet rapidly remodels islet sympathetic innervation while long-term high fat diet results in islet-specific cholinergic neuropathy. Using highly targeted, organ- and circuit-specific approaches, we demonstrate that remodeling of pancreatic innervation contributes to impaired glycemic control with short- and long-term nutrient excess. Counteracting the nutrient-induced changes in sympathetic and parasympathetic inputs to the pancreas using neuromodulation and repurposed FDA-approved approaches, we can significantly improve glycemic control even with long-term high fat diet. Finally, we identify islet Schwann cells as a source of the neurotrophic factor, S100b, contributing to rapid sympathetic hyperinnervation with short-term overnutrition. Our findings reveal novel adaptations in islet innervation contributing to nutrition-mediated metabolic dysfunction that can be ameliorated by targeting pancreatic neural circuits.

physiology↗

bioRxiv2025

Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers

Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases--SILVA, Greengenes2, RDP, NCBI RefSeq, and GTDB--against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results revealed that the use of the weighting method significantly improved both classification counts and fully classified ratios, along with a substantial (P < 0.05) reduction in error rates compared to unweighted taxonomy classifier. While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with substantial error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.

bioinformatics↗

bioRxiv2024

Combined inhibition of S100A4 and TIGIT suppresses late-stage breast cancer metastasis to the lung by activating T and NK cells

Cancer metastasis is responsible for approximately 90% of cancer-related deaths, but very few treatment options exist currently. While the role of S100A4 in promoting metastasis has been known for decades, this knowledge has not been translated in the clinic. Here, we report that a novel monoclonal antibody against the human S100A4 protein (S1004-11) effectively suppresses breast cancer metastasis in two different mouse models. Importantly, a novel combination of ant-TIGIT and S100A4-11 can suppress lung metastases even in late-stage disease after the lung premetastatic niche (PMN) has already been established similar to a stage when many breast cancer patients are diagnosed. Mechanistically, S1004-11 mAb treatment block the formation of PMN by suppressing neutrophil infiltration and activating natural killer (NK) and T cells in the lung. Single-cell RNA-sequencing and cell:cell communication analyses indicate that TIGIT signaling suppresses NK cells, which is reversed in S100A4-11 treated PMN. In summary, this study provides compelling evidence for a novel mechanism of S100A4 function in PMN formation and the feasibility of using S100A4-11 monoclonal antibody to suppress metastases at different stages of breast cancer progression.

cancer biology↗

bioRxiv2024

LGR4 is essential for maintaining beta-cell homeostasis through suppression of RANK

Pancreatic {beta}-cell stress contributes to diabetes progression. This study demonstrates that Leucine-rich repeat-containing G-protein-coupled-receptor-4 (LGR4) is critical for maintaining {beta}-cell health and is modulated by stressors. In vitro, Lgr4 knockdown decreases proliferation and survival in rodent {beta}-cells, while overexpression protects against cytokine-induced cell death in rodent and human {beta}-cells. Mechanistically, LGR4 suppresses Receptor Activator of Nuclear Factor Kappa B (NF{kappa}B) (RANK) and its subsequent activation of NF{kappa}B to protect {beta}-cells. {beta}-cell-specific Lgr4-conditional knockout (cko) mice exhibit normal glucose homeostasis but increased {beta}-cell death in both sexes and decreased proliferation only in females. Male Lgr4cko mice under stress display reduced {beta}-cell proliferation and a further increase in {beta}-cell death. Upon aging, both male and female Lgr4cko mice display impaired {beta}-cell homeostasis, however, only female mice are glucose intolerant with decreased plasma insulin. We show that LGR4 is required for maintaining {beta}-cell health under basal and stress-induced conditions, through suppression of RANK. TeaserLGR4 receptor is critical for maintaining {beta}-cell health under basal and stressed conditions, through suppression of RANK.

physiology↗

bioRxiv2023

Single Cell RNA-Seq Analysis of Regenerative Drug-Treated Human Pancreatic Islets Identifies A Cycling Alpha Cell Population As Key Beta Cell Progenitors

Diabetes ultimately results from an inadequate number of functional, insulin-producing human beta cells. Although current attempts to replenish the remaining beta cell pool in people with diabetes are encouraging, scalability and cost limit access for the millions of people with diabetes. The small molecule DYRK1A inhibitor class of beta cell regenerative drugs, either alone or in combination with GLP1 receptor agonists or TGF{beta} superfamily inhibitors, are capable of inducing beta cell replication in vitro and increasing beta cell mass in vivo. Despite these advances, the precise mechanisms of action of DYRK1A inhibitors remain incompletely understood. To address the mechanisms more deeply, we performed single cell RNA sequencing on human pancreatic islets treated with a DYRK1A inhibitor, either alone, or in combination with a GLP1 receptor agonist or a TGF{beta} superfamily inhibitor. We identify a cluster of Cycling Alpha Cells as the cells most responsive to DYRK1A inhibition. Velocity and pseudotime lineage trajectory analyses suggest that Cycling Alpha Cells serve as the primary target cell type for of DYRK1A inhibitors, and may serve as precursor cells that transdifferentiate into functional human beta cells in response to the DYRK1A inhibition. In addition to providing a novel mechanism of action for DYRK1A inhibitors, our findings suggest that efforts to target regenerative drugs to human beta cells may be mis-directed: the proper target may be Cycling Alpha Cells.

cell biology↗

bioRxiv2023

Sequence-based prediction of the solubility of peptides containing non-natural amino acids

Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs, as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the solubility of mAA-containing peptides. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different mAAs for a total number of 30 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm.

biophysics↗

bioRxiv2022

High-quality nuclear genome and mitogenome of Bipolaris sorokiniana strain LK93, a devastating pathogen causing wheat root rot

Bipolaris sorokiniana, one of the most devastating hemibiotrophic fungal pathogens, causes root rot, crown rot, leaf blotching, and black embryos of gramineous crops worldwide, posing a serious threat to global food security. However, the host-pathogen interaction mechanism between B. sorokiniana and wheat remains poorly understood. To facilitate related studies, we sequenced and assembled the genome of B. sorokiniana strain LK93. Nanopore long reads and next generation sequencing short reads were applied in the genome assembly, and the final 36.4 Mb genome assembly contains 16 contigs with the contig N50 of 2.3 Mb. Subsequently, we annotated 11,811 protein-coding genes including 10,620 functional genes, 258 of which were identified as secretory proteins including 211 predicted effectors. Additionally, the 111,581 bp mitogenome of LK93 was assembled and annotated. The LK93 genomes presented in this study will facilitate research in the B. sorokiniana-wheat pathosystem for better control of crop diseases.

plant biology↗

bioRxiv2022

Genetic dissection of crossover mutants defines discrete intermediates in mouse meiosis

Crossovers, the exchange of homolog arms, are required for accurate segregation during meiosis. Studies in yeast have established that the single end invasion intermediate is highly regulated to ensure crossover distribution. Single end invasions are thought to differentiate into double Holliday junctions that are resolved by MutLgamma (MLH1/3) into crossovers. Currently, we lack knowledge of early steps of mammalian crossover recombination or how intermediates are differentiated in any organism. Using comprehensive analysis of recombination and cytology, we infer that polymerized single-end invasion intermediates and nicked double Holliday junctions are crossover precursors in mouse spermatocytes. In marked contrast to yeast, MLH3 plays a structural role to differentiate single end invasions into double Holliday junctions with differentially polymerized 3 ends. Therefore, we show independent genetic requirements for precursor formation and asymmetry with regard to 3 end processing, providing mechanistic insight into crossover formation and patterning.

genetics↗

bioRxiv2022

Sequence-based pH-dependent prediction of protein solubility using CamSol

Solubility is a property of central importance for the use of proteins in research and in applications in biotechnology and medicine. Since experimental methods for measuring protein solubility are resource-intensive and time-consuming, computational methods have recently emerged to enable the rapid and inexpensive screening of large libraries of proteins, as it is routinely required in development pipelines. Here, we describe the extension of one of such methods, CamSol, to include in the predictions the effect of the pH of the solubility. We illustrate the accuracy of the pH-dependent predictions on a variety of antibodies and other proteins.

biophysics↗

bioRxiv2022

Extracellular matrix guidance determines proteolytic and non-proteolytic cancer cell patterning

Metastatic tumor cell invasion into interstitial tissue is a mechanochemical process that responds to tissue cues and further involves proteolytic remodeling of the tumor stroma. How matrix density, tissue guidance and the ability of proteolytic tissue remodeling cooperate and determine decision-making of invading tumor cells in complex-structured three-dimensional (3D) tissue remains unclear. We here developed a collagen-based invasion assay containing a guiding interface of low collagen density adjacent to randomly organized 3D fibrillar lattice and examined the invasion of melanoma cells from multicellular spheroids in response to matrix density, guidance cues and collagenolysis. After 48 hours of culture, two invasion niches developed, (i) sheet-like collective migration along the interface and (ii) single cell- and strand-like invasion into randomly organized 3D matrix. High collagen density impeded migration into the random matrix, whereas migration along a high-density collagen interface was increased compared to the low-density matrix assay. In silico analysis predicted that facilitated interface migration in high-density matrix depended on physical guidance without collagen degradation, whereas migration into randomly organized matrix was strongly dependent on collagenolysis. When tested in 3D culture, inhibition of matrix metalloprotease (MMP)-mediated collagen degradation compromised migration into random matrix in dependence of density, whereas interface-guided migration remained effective. In conclusion, with increasing tissue density, matrix cues bordered by dense matrix, but not randomly organized matrix, support effective MMP-independent migration. This identifies the topology of interstitial tissue a primary determinant of switch behaviors between MMP-dependent and MMP-independent cancer cell invasion.

cancer biology↗

bioRxiv2021

The timescale and magnitude of aperiodic activity decreases with cortical depth in humans, macaques and mice

Cortical dynamics obey a 1/f power law, exhibiting an exponential decay of spectral power with increasing frequency. The slope and offset of this 1/f decay reflect the timescale and magnitude of aperiodic neural activity, respectively. These properties are tightly linked to cellular and circuit mechanisms (e.g. excitation:inhibition balance and firing rates) as well as cognitive processes (e.g. perception, memory, and state). However, the physiology underlying the 1/f power law in cortical dynamics is not well understood. Here, we compared laminar recordings from human, macaque and mouse cortex to evaluate how 1/f aperiodic dynamics vary across cortical layers and species. We report that 1/f slope is steepest in superficial layers and flattest in deep layers in each species. Additionally, the magnitude of this 1/f decay is greatest in superficial cortex and decreases with depth. We could account for both of these findings with a simple model in which superficial cortical transmembrane currents had longer time constants and greater densities than those in deeper layers. Together, our results provide novel insight into the organization of cortical dynamics, suggesting that the amplitude and time constant of local currents control circuit processing as a function of laminar depth. This may represent a general mechanism to facilitate appropriate integration of fast sensory inputs (infragranular) with slow feedback-type inputs (supragranular) across cortical areas and species.

neuroscience↗